X-128383343-C-T

Position:

• chrX-128383343-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000449485.2(ENSG00000225689):​n.412-46971G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.99 (38407 hom., 33137 hem., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000225689 ENST00000449485.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95

Genes affected

ENSG00000225689 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985698	XR_002958819.2	n.1125-46971G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000225689	ENST00000449485.2	n.412-46971G>A		intron_variant		5
ENSG00000225689	ENST00000657074.1	n.3400-46971G>A		intron_variant
ENSG00000225689	ENST00000660383.1	n.927-46971G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.00 AC: 110404 AN: 111121 Hom.: 38411 Cov.: 24 AF XY: 0.994 AC XY: 33072 AN XY: 33271 FAILED QC

Gnomad AFR AF: 0.978

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.996

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 1.00

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.995

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.994 AC: 110460 AN: 111176 Hom.: 38407 Cov.: 24 AF XY: 0.994 AC XY: 33137 AN XY: 33336

Gnomad4 AFR AF: 0.978

Gnomad4 AMR AF: 0.996

Gnomad4 ASJ AF: 1.00

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 1.00

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 1.00

Gnomad4 OTH AF: 0.995

Alfa AF: 0.996 Hom.: 11249

Bravo AF: 0.992

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.85
DANN	Benign	0.55

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2340419; hg19: chrX-127517321;